/*
 * Copyright (c) <2008 - 2020>, University of Washington, Simon Fraser University, Bilkent University
 * All rights reserved.
 *
 * Redistribution and use in source and binary forms, with or without modification,
 * are permitted provided that the following conditions are met:
 *
 * Redistributions of source code must retain the above copyright notice, this list
 * of conditions and the following disclaimer.
 * - Redistributions in binary form must reproduce the above copyright notice, this
 *   list of conditions and the following disclaimer in the documentation and/or other
 *   materials provided with the distribution.
 * - Neither the names of the University of Washington, Simon Fraser University, 
 *   nor the names of its contributors may be
 *   used to endorse or promote products derived from this software without specific
 *   prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
 * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
 * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
 * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
 * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
 * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
 * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
 * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

/*
  Authors: 
  Farhad Hormozdiari
  Faraz Hach
  Can Alkan
  Emails: 
  farhadh AT uw DOT edu
  fhach AT cs DOT sfu DOT ca
  calkan AT cs DOT bilkent DOT edu DOT tr
*/



#ifndef __OUTPUT__
#define __OUTPUT__

#define	FORWARD 0
#define REVERSE 1

typedef struct
{
  char		*tag;
  char		type;
  char		cVal;
  int		iVal;
  float		fVal;
  char		*sVal;
} OPT_FIELDS;

typedef struct  
{
  char			*QNAME;
  short			FLAG;
  char			*RNAME;
  int			POS;
  unsigned char  	MAPQ;
  char			*CIGAR;
  char			*MRNAME;
  int			MPOS;
  int			ISIZE;
  char			*SEQ;
  char			*QUAL;
  int			optSize;
  OPT_FIELDS	        *optFields;
} SAM;

int initOutput(char *fileName, int compressed);
void (*finalizeOutput)();
void (*output)(SAM map);
void outputSAM(FILE *fp, SAM map);

FILE * getOutputFILE();
void SAMheaderTX(FILE *);
void SAMheaderGZ(gzFile);

#endif
